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For: Wang YF, Tie Y, Boross PI, Tozser J, Ghosh AK, Harrison RW, Weber IT. Potent new antiviral compound shows similar inhibition and structural interactions with drug resistant mutants and wild type HIV-1 protease. J Med Chem 2007;50:4509-15. [PMID: 17696515 PMCID: PMC2751596 DOI: 10.1021/jm070482q] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Number Cited by Other Article(s)
1
Peng C, Wang J, Xu Z, Cai T, Zhu W. Accurate prediction of relative binding affinities of a series of HIV-1 protease inhibitors using semi-empirical quantum mechanical charge. J Comput Chem 2020;41:1773-1780. [PMID: 32352193 DOI: 10.1002/jcc.26218] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 04/03/2020] [Accepted: 04/18/2020] [Indexed: 11/05/2022]
2
Design and biological evaluation of novel HIV-1 protease inhibitors with isopropanol as P1' ligand to enhance binding with S1' subsite. Bioorg Med Chem 2020;28:115623. [PMID: 32690263 DOI: 10.1016/j.bmc.2020.115623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 06/27/2020] [Accepted: 06/27/2020] [Indexed: 10/23/2022]
3
Zhu M, Dou Y, Ma L, Dong B, Zhang F, Zhang G, Wang J, Zhou J, Cen S, Wang Y. Novel HIV-1 Protease Inhibitors with Morpholine as the P2 Ligand to Enhance Activity against DRV-Resistant Variants. ACS Med Chem Lett 2020;11:1196-1204. [PMID: 32551001 DOI: 10.1021/acsmedchemlett.0c00043] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 03/31/2020] [Indexed: 11/29/2022]  Open
4
Grillo IB, Urquiza‐Carvalho GA, Chaves EJF, Rocha GB. Semiempirical methods do Fukui functions: Unlocking a modeling framework for biosystems. J Comput Chem 2020;41:862-873. [DOI: 10.1002/jcc.26148] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/15/2019] [Accepted: 01/01/2020] [Indexed: 01/16/2023]
5
Karnati KR, Wang Y. Structural and binding insights into HIV-1 protease and P2-ligand interactions through molecular dynamics simulations, binding free energy and principal component analysis. J Mol Graph Model 2019;92:112-122. [PMID: 31351319 DOI: 10.1016/j.jmgm.2019.07.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 07/16/2019] [Accepted: 07/17/2019] [Indexed: 12/15/2022]
6
Gao Y, Zhu T, Chen J. Exploring drug-resistant mechanisms of I84V mutation in HIV-1 protease toward different inhibitors by thermodynamics integration and solvated interaction energy method. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.06.040] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
7
Funicello M, Chiummiento L, Tramutola F, Armentano M, Bisaccia F, Miglionico R, Milella L, Benedetti F, Berti F, Lupattelli P. Synthesis and biological evaluation in vitro and in mammalian cells of new heteroaryl carboxyamides as HIV-protease inhibitors. Bioorg Med Chem 2017;25:4715-4722. [DOI: 10.1016/j.bmc.2017.07.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 06/30/2017] [Accepted: 07/06/2017] [Indexed: 11/16/2022]
8
Ngo ST, Nguyen MT, Nguyen MT. Determination of the absolute binding free energies of HIV-1 protease inhibitors using non-equilibrium molecular dynamics simulations. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.03.034] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
9
Fast and accurate determination of the relative binding affinities of small compounds to HIV-1 protease using non-equilibrium work. J Comput Chem 2016;37:2734-2742. [DOI: 10.1002/jcc.24502] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 08/29/2016] [Accepted: 09/06/2016] [Indexed: 02/06/2023]
10
Ghosh AK, Osswald HL, Prato G. Recent Progress in the Development of HIV-1 Protease Inhibitors for the Treatment of HIV/AIDS. J Med Chem 2016;59:5172-208. [PMID: 26799988 PMCID: PMC5598487 DOI: 10.1021/acs.jmedchem.5b01697] [Citation(s) in RCA: 282] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
11
Meher BR, Wang Y. Exploring the drug resistance of V32I and M46L mutant HIV-1 protease to inhibitor TMC114: flap dynamics and binding mechanism. J Mol Graph Model 2014;56:60-73. [PMID: 25562662 DOI: 10.1016/j.jmgm.2014.11.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 10/14/2014] [Accepted: 11/07/2014] [Indexed: 12/22/2022]
12
Ghosh AK, Yashchuk S, Mizuno A, Chakraborty N, Agniswamy J, Wang YF, Aoki M, Gomez PMS, Amano M, Weber IT, Mitsuya H. Design of gem-difluoro-bis-tetrahydrofuran as P2 ligand for HIV-1 protease inhibitors to improve brain penetration: synthesis, X-ray studies, and biological evaluation. ChemMedChem 2014;10:107-15. [PMID: 25336073 DOI: 10.1002/cmdc.201402358] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Indexed: 01/10/2023]
13
Bonini C, Chiummiento L, Di Blasio N, Funicello M, Lupattelli P, Tramutola F, Berti F, Ostric A, Miertus S, Frecer V, Kong DX. Synthesis and biological evaluation of new simple indolic non peptidic HIV Protease inhibitors: The effect of different substitution patterns. Bioorg Med Chem 2014;22:4792-802. [DOI: 10.1016/j.bmc.2014.06.055] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 06/25/2014] [Accepted: 06/30/2014] [Indexed: 11/30/2022]
14
Weber IT, Waltman MJ, Mustyakimov M, Blakeley MP, Keen DA, Ghosh AK, Langan P, Kovalevsky AY. Joint X-ray/neutron crystallographic study of HIV-1 protease with clinical inhibitor amprenavir: insights for drug design. J Med Chem 2013;56:5631-5. [PMID: 23772563 DOI: 10.1021/jm400684f] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
15
Meher BR, Wang Y. Binding of single walled carbon nanotube to WT and mutant HIV-1 proteases: analysis of flap dynamics and binding mechanism. J Mol Graph Model 2012;38:430-45. [PMID: 23142620 DOI: 10.1016/j.jmgm.2012.10.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 08/31/2012] [Accepted: 10/05/2012] [Indexed: 10/27/2022]
16
Eissenstat M, Guerassina T, Gulnik S, Afonina E, Silva AM, Ludtke D, Yokoe H, Yu B, Erickson J. Enamino-oxindole HIV protease inhibitors. Bioorg Med Chem Lett 2012;22:5078-83. [PMID: 22749283 DOI: 10.1016/j.bmcl.2012.05.120] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Revised: 05/30/2012] [Accepted: 05/30/2012] [Indexed: 10/28/2022]
17
Ghosh AK, Anderson DD, Weber IT, Mitsuya H. Enhancing protein backbone binding--a fruitful concept for combating drug-resistant HIV. Angew Chem Int Ed Engl 2012;51:1778-802. [PMID: 22290878 PMCID: PMC7159617 DOI: 10.1002/anie.201102762] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Indexed: 12/02/2022]
18
Meher BR, Wang Y. Interaction of I50V mutant and I50L/A71V double mutant HIV-protease with inhibitor TMC114 (darunavir): molecular dynamics simulation and binding free energy studies. J Phys Chem B 2012;116:1884-900. [PMID: 22239286 DOI: 10.1021/jp2074804] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
19
Ghosh AK, Anderson DD. Tetrahydrofuran, tetrahydropyran, triazoles and related heterocyclic derivatives as HIV protease inhibitors. Future Med Chem 2011;3:1181-97. [PMID: 21806380 PMCID: PMC3164575 DOI: 10.4155/fmc.11.68] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]  Open
20
Ghosh AK, Martyr CD, Steffey M, Wang YF, Agniswamy J, Amano M, Weber IT, Mitsuya H. Design of substituted bis-Tetrahydrofuran (bis-THF)-derived Potent HIV-1 Protease Inhibitors, Protein-ligand X-ray Structure, and Convenient Syntheses of bis-THF and Substituted bis-THF Ligands. ACS Med Chem Lett 2011;2:298-302. [PMID: 22509432 DOI: 10.1021/ml100289m] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]  Open
21
Shen CH, Wang YF, Kovalevsky AY, Harrison RW, Weber IT. Amprenavir complexes with HIV-1 protease and its drug-resistant mutants altering hydrophobic clusters. FEBS J 2010;277:3699-714. [PMID: 20695887 DOI: 10.1111/j.1742-4658.2010.07771.x] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
22
Das D, Koh Y, Tojo Y, Ghosh AK, Mitsuya H. Prediction of potency of protease inhibitors using free energy simulations with polarizable quantum mechanics-based ligand charges and a hybrid water model. J Chem Inf Model 2010;49:2851-62. [PMID: 19928916 DOI: 10.1021/ci900320p] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
23
Hu GD, Zhu T, Zhang SL, Wang D, Zhang QG. Some insights into mechanism for binding and drug resistance of wild type and I50V V82A and I84V mutations in HIV-1 protease with GRL-98065 inhibitor from molecular dynamic simulations. Eur J Med Chem 2010;45:227-35. [DOI: 10.1016/j.ejmech.2009.09.048] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2009] [Revised: 09/30/2009] [Accepted: 09/30/2009] [Indexed: 11/30/2022]
24
Approaches to the design of HIV protease inhibitors with improved resistance profiles. Curr Opin HIV AIDS 2009;3:633-41. [PMID: 19373035 DOI: 10.1097/coh.0b013e328313911d] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
25
New approaches to HIV protease inhibitor drug design II: testing the substrate envelope hypothesis to avoid drug resistance and discover robust inhibitors. Curr Opin HIV AIDS 2009;3:642-6. [PMID: 19373036 DOI: 10.1097/coh.0b013e3283136cee] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
26
Ghosh AK, Kulkarni S, Anderson DD, Hong L, Baldridge A, Wang YF, Chumanevich AA, Kovalevsky AY, Tojo Y, Koh Y, Tang J, Weber IT, Mitsuya H, Mitsuya H. Design, synthesis, protein-ligand X-ray structure, and biological evaluation of a series of novel macrocyclic human immunodeficiency virus-1 protease inhibitors to combat drug resistance. J Med Chem 2009;52:7689-705. [PMID: 19746963 PMCID: PMC2943150 DOI: 10.1021/jm900695w] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
27
Ghosh AK, Leshchenko-Yashchuk S, Anderson DD, Baldridge A, Noetzel M, Miller HB, Tie Y, Wang YF, Koh Y, Weber IT, Mitsuya H. Design of HIV-1 protease inhibitors with pyrrolidinones and oxazolidinones as novel P1'-ligands to enhance backbone-binding interactions with protease: synthesis, biological evaluation, and protein-ligand X-ray studies. J Med Chem 2009;52:3902-14. [PMID: 19473017 PMCID: PMC2745609 DOI: 10.1021/jm900303m] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
28
Lapins M, Wikberg JES. Proteochemometric Modeling of Drug Resistance over the Mutational Space for Multiple HIV Protease Variants and Multiple Protease Inhibitors. J Chem Inf Model 2009;49:1202-10. [DOI: 10.1021/ci800453k] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
29
Structural and Kinetic Analysis of Pyrrolidine-Based Inhibitors of the Drug-Resistant Ile84Val Mutant of HIV-1 Protease. J Mol Biol 2008;383:347-57. [DOI: 10.1016/j.jmb.2008.07.062] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2008] [Revised: 07/22/2008] [Accepted: 07/24/2008] [Indexed: 11/17/2022]
30
Ghosh AK, Gemma S, Baldridge A, Wang YF, Kovalevsky AY, Koh Y, Weber IT, Mitsuya H. Flexible cyclic ethers/polyethers as novel P2-ligands for HIV-1 protease inhibitors: design, synthesis, biological evaluation, and protein-ligand X-ray studies. J Med Chem 2008;51:6021-33. [PMID: 18783203 PMCID: PMC2812926 DOI: 10.1021/jm8004543] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
31
Giffin MJ, Heaslet H, Brik A, Lin YC, Cauvi G, Wong CH, McRee DE, Elder JH, Stout CD, Torbett BE. A copper(I)-catalyzed 1,2,3-triazole azide-alkyne click compound is a potent inhibitor of a multidrug-resistant HIV-1 protease variant. J Med Chem 2008;51:6263-70. [PMID: 18823110 DOI: 10.1021/jm800149m] [Citation(s) in RCA: 192] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
32
Kovalevsky AY, Louis JM, Aniana A, Ghosh AK, Weber IT. Structural evidence for effectiveness of darunavir and two related antiviral inhibitors against HIV-2 protease. J Mol Biol 2008;384:178-92. [PMID: 18834890 DOI: 10.1016/j.jmb.2008.09.031] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2008] [Revised: 08/25/2008] [Accepted: 09/09/2008] [Indexed: 10/21/2022]
33
Ghosh AK, Gemma S, Takayama J, Baldridge A, Leshchenko-Yashchuk S, Miller HB, Wang YF, Kovalevsky AY, Koh Y, Weber IT, Mitsuya H. Potent HIV-1 protease inhibitors incorporating meso-bicyclic urethanes as P2-ligands: structure-based design, synthesis, biological evaluation and protein-ligand X-ray studies. Org Biomol Chem 2008;6:3703-13. [PMID: 18843400 DOI: 10.1039/b809178a] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
34
Effect of flap mutations on structure of HIV-1 protease and inhibition by saquinavir and darunavir. J Mol Biol 2008;381:102-15. [PMID: 18597780 DOI: 10.1016/j.jmb.2008.05.062] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2008] [Revised: 05/13/2008] [Accepted: 05/14/2008] [Indexed: 11/20/2022]
35
Purohit R, Rajasekaran R, Sudandiradoss C, George Priya Doss C, Ramanathan K, Rao S. Studies on flexibility and binding affinity of Asp25 of HIV-1 protease mutants. Int J Biol Macromol 2008;42:386-91. [DOI: 10.1016/j.ijbiomac.2008.01.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2007] [Revised: 01/26/2008] [Accepted: 01/28/2008] [Indexed: 11/30/2022]
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